CSC's trainings and events have moved

Find our upcoming trainings and events at www.csc.fi.

This site is an archive version and is no longer updated.
 

Go to CSC Customer trainings and Events

null RNA-seq data analysis workshop
RNA-seq data analysis workshop
Date: 08.01.2014 12:00 - 11.01.2014 16:00
Location details: -
Language: english-language
lecturers: Several speakers as indicated in the program.
Price: -
This international workshop covers several aspects of RNA-seq data analysis, ranging from quality control, assembly and alignment to differential expression analysis and miRNA-mRNA integration. Particular emphasis is given to comparison of different analysis tools. The program consists of two lecture days and four optional hands-on sessions.
 

This workshop is kindly sponsored by the FP7 AllBio project, which aims to bring biologists and bioinformaticians together for the effective exploitation of high-throughput data.

Program

Tuesday 7.1.2014

Coffee

FULL! 12:00-15:00 Additional hands-on tutorial 3: RNA-seq data analysis using Chipster (Eija Korpelainen)
This tutorial covers quality control (FastQC and PRINSEQ), alignment (TopHat) and quantification (HTSeq) as well as differential expression analysis (edgeR and DESeq) and genome browser visualization. The user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required and the tutorial is thus suitable for everybody.

 

Wednesday 8.1.2014

Registration and coffee

10:00 Welcome (Eija Korpelainen, CSC)

Session I: Quality control and alignment

  • 10:15-11:05 Quality checking and pre-processing your RNA-seq data (Mikael Huss, SciLifelab, Sweden)

Lunch

Session II: Reliability of RNA-seq, differential expression analysis

  • 13:00-13:45 Reliability and interpretation of RNA-Seq expression profiles (Pawel Labaj, BOKU, Austria)
  • 13:45-14:20 Transcript isoform expression and differential expression estimation with BitSeq (Antti Honkela, University of Helsinki, Finland)
  • 14:20-15:00 Comparison of differential expression analysis tools (Laura Elo, University of Turku, Finland)
Coffee
 
FULL! 15:00-18:00 Hands-on tutorial 1: Differential expression analysis using R/Bioconductor and Unix (Mikael Huss, Pär Engström)
This hands-on session covers quantification and differential expression analysis of RNA-seq data. The analysis tools used in the exercises include command line applications and Bioconductor packages such as Cuffdiff and DESeq2, so participants need to be familiar with Unix and R. The instructions can be found here.

 

Thursday 9.1.2014

Coffee

Session III: Transcriptome assembly

  • 10:00-10:30 Introduction to transcriptome assembly (Panu Somervuo, University of Helsinki, Finland)
Session IV: miRNA-seq data analysis
  • 11:30-12:20 Introduction to small RNA sequence analysis with applications in nematodes (Garry Wong, UEF, Finland)

Lunch

  • 13:20-14:00 Small RNA data analysis and miRNA discovery in plants and mammalians (Andreas Gisel, ITB, Italy)
  • 14:00-14:50 Joint analysis of miRNA and mRNA expression data (Angel Rubio, CEIT, Spain)

Coffee
 
FULL! 15:00-18:00 Hands-on tutorial 2: Small RNA data analysis (Andreas Gisel)
This tutorial covers a command line based workflow to find known and novel miRNAs using tools like BWA and mirDeep2, so participants should be familiar with Unix. The workflow is developed at ITB, Italy, and it reports the results in a graphical form allowing an easy way to extract the required information.

 

Friday 10.1.2014

Coffee

FULL! 9:00-12:00 Hands-on tutorial 3: RNA-seq data analysis using Chipster (Eija Korpelainen)
This tutorial covers quality control (FastQC and PRINSEQ), alignment (TopHat) and quantification (HTSeq) as well as differential expression analysis (edgeR and DESeq) and genome browser visualization. The user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required and the tutorial is thus suitable for everybody.

Lunch

FULL! 13:00-16:00 Hands-on tutorial 4: Using cluster and grid computing in RNA-seq data-analysis (Kimmo Mattila)
This tutorial demonstrates how researchers working in Finland can utilize the cluster capacity of CSC and the FGI grid environment for computationally demanding analysis tasks. In these environments you can run tools like Trinity or TopHat using tens or hundreds of computing cores. The knowledge of Unix is required for this session.